Generate a complete LAMMPS input script for molecular dynamics simulation.

Creates a ready-to-run LAMMPS input file with support for LJ, EAM, Tersoff, Buckingham, and Coulomb potentials. Ensembles: NVT, NPT, NVE, NPH. Optional energy minimization and shear deformation.

Args: atoms_per_side: Number of unit cells per side of the cubic box. lattice_spacing: Lattice constant in Angstroms. potential: Interatomic potential type (lj, eam, tersoff, buckingham, coulomb). epsilon: LJ energy parameter. sigma: LJ length parameter. cutoff: Pair potential cutoff distance. ensemble: Thermodynamic ensemble (nvt, npt, nve, nph). temperature: Target temperature. pressure: Target pressure (for NPT/NPH). timestep: Integration timestep. n_steps: Total number of MD steps. dump_freq: Frequency of trajectory dumps. minimize: Run energy minimization before dynamics. apply_shear: Apply shear deformation during dynamics. shear_rate: Shear strain rate. shear_direction: Shear plane (xy, xz, yz). boundary: Boundary conditions. output_file: If provided, write script to this file.

Generate a multi-step LAMMPS workflow (minimize → equilibrate → production).

Creates a complete input script with three sequential phases:

1. Energy minimization (optional)

2. Equilibration (NVT or NPT)

3. Production run (with optional shear)

Args: atoms_per_side: Number of unit cells per side. lattice_spacing: Lattice constant. potential: Interatomic potential type. epsilon: LJ energy parameter. sigma: LJ length parameter. cutoff: Pair potential cutoff. timestep: Integration timestep. n_minimize_steps: Number of minimization steps (0 to skip). n_equilibrate_steps: Number of equilibration steps. equilibrate_temp: Temperature for equilibration. equilibrate_ensemble: Ensemble for equilibration. n_production_steps: Number of production steps. production_temp: Temperature for production. production_ensemble: Ensemble for production. production_pressure: Pressure for production (if NPT). apply_shear: Apply shear during production. shear_rate: Shear strain rate. shear_direction: Shear plane (xy, xz, yz). dump_freq: Dump frequency during production. thermo_freq: Thermodynamic output frequency. output_file: Optional file path to write the script.

Parse LAMMPS thermodynamic output and return time-series data.

Reads a LAMMPS log file or thermo.dat file and extracts columns like Step, Temp, PotEng, TotEng, Press, etc.

Args: filepath: Path to the LAMMPS thermo output file.

Parse a LAMMPS dump file and return trajectory frame summaries.

Reads lammpstrj files and extracts atom positions, box dimensions, and metadata for each frame.

Args: filepath: Path to the LAMMPS dump file. max_frames: Maximum number of frames to parse (0 = all).

Get a summary of a LAMMPS output file (dump or thermo).

Identifies the file type and returns key statistics: number of frames, atoms, columns, box dimensions, or thermo time-series stats.

Args: filepath: Path to the LAMMPS output file.

Compute the scalar nematic order parameter S from quaternion data.

S measures alignment of anisotropic particles. S=1 is perfect alignment, S=0 is isotropic, S=-0.5 is perpendicular alignment.

Input is a JSON array of quaternions [w, x, y, z] for each particle.

Args: quaternions_json: JSON string with shape (N, 4) quaternion data. Example: "[[1,0,0,0], [0.9,0.1,0,0], [0.8,0.2,0.1,0]]"

Compute nematic alignment profile S(z) along the z-axis.

Bins particles by z-coordinate and computes S in each bin, useful for studying alignment near surfaces or interfaces.

Args: quaternions_json: JSON string with shape (N, 4) quaternion data. z_positions_json: JSON string with shape (N,) z-coordinates. n_bins: Number of bins along z.

Compute nematic alignment S(t) over a trajectory.

Each frame contains quaternions for all particles at that timestep.

Args: quaternions_frames_json: JSON string — list of (N, 4) arrays, one per frame. Example: "[[[1,0,0,0],[0.9,0.1,0,0]], [[0.8,0.2,0.1,0],[0.7,0.3,0,0]]]"

Compute non-affine displacement D²min for each particle between two frames.

D²min measures how much a particle's displacement deviates from the best-fit affine deformation of its neighbors. High D²min = plastic event.

Args: positions_t0_json: JSON string, shape (N, 3) positions at time t0. positions_t1_json: JSON string, shape (N, 3) positions at time t1. r_cut: Cutoff radius for neighbor finding.

Identify particles that underwent plastic rearrangement.

Args: d2min_json: JSON string with D²min values for each particle. threshold: D²min threshold for plastic events.

Generate LAMMPS input scripts for a shear-rate sweep.

Creates one input script per shear rate to study rheological behavior, shear thinning/thickening, and viscosity as a function of shear rate.

Args: shear_rates: JSON array of shear rates to simulate. atoms_per_side: Number of unit cells per side. lattice_spacing: Lattice constant. potential: Interatomic potential type. temperature: Simulation temperature. n_equilibrate: Number of equilibration steps. n_production: Number of production steps. shear_direction: Shear plane (xy, xz, yz). output_dir: Directory to write scripts.

Estimate viscosity from shear rate vs shear stress data.

Fits a power-law model: stress = K * rate^n, where n=1 is Newtonian, n<1 is shear-thinning, n>1 is shear-thickening.

Args: shear_rates_json: JSON array of shear rates. shear_stresses_json: JSON array of corresponding shear stresses.